data_9R23
#
_model_server_result.job_id            LOi7UcjwGaAVIVQVYQ12cA 
_model_server_result.datetime_utc      '2025-08-01 13:35:51' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          9r23 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"XB","auth_seq_id":314}' 
#
_entry.id    9R23 
#
_exptl.entry_id    9R23 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              284.436 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            RETINAL 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            9R23 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9R23 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 O N N 
? 3 GA N N 
? 3 UA N N 
? 3 HB N N 
? 3 XB N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A NZ LYS 213 A LYS 213 1_555 O C15 RET . A RET 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? 
covale ? covale2 B NZ LYS 213 B LYS 213 1_555 GA C15 RET . B RET 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? 
covale ? covale3 C NZ LYS 213 C LYS 213 1_555 UA C15 RET . C RET 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? 
covale ? covale4 D NZ LYS 213 D LYS 213 1_555 HB C15 RET . D RET 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? 
covale ? covale5 E NZ LYS 213 E LYS 213 1_555 XB C15 RET . E RET 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? 
#
_chem_comp.formula           'C20 H28 O' 
_chem_comp.formula_weight    284.436 
_chem_comp.id                RET 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              RETINAL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
C1 C2 RET sing 338 n n 
C1 C6 RET sing 339 n n 
C1 C16 RET sing 340 n n 
C1 C17 RET sing 341 n n 
C2 C3 RET sing 342 n n 
C2 H21 RET sing 343 n n 
C2 H22 RET sing 344 n n 
C3 C4 RET sing 345 n n 
C3 H31 RET sing 346 n n 
C3 H32 RET sing 347 n n 
C4 C5 RET sing 348 n n 
C4 H41 RET sing 349 n n 
C4 H42 RET sing 350 n n 
C5 C6 RET doub 351 n n 
C5 C18 RET sing 352 n n 
C6 C7 RET sing 353 n n 
C7 C8 RET doub 354 e n 
C7 H7 RET sing 355 n n 
C8 C9 RET sing 356 n n 
C8 H8 RET sing 357 n n 
C9 C10 RET doub 358 e n 
C9 C19 RET sing 359 n n 
C10 C11 RET sing 360 n n 
C10 H10 RET sing 361 n n 
C11 C12 RET doub 362 e n 
C11 H11 RET sing 363 n n 
C12 C13 RET sing 364 n n 
C12 H12 RET sing 365 n n 
C13 C14 RET doub 366 e n 
C13 C20 RET sing 367 n n 
C14 C15 RET sing 368 n n 
C14 H14 RET sing 369 n n 
C15 O1 RET doub 370 n n 
C15 H15 RET sing 371 n n 
C16 H161 RET sing 372 n n 
C16 H162 RET sing 373 n n 
C16 H163 RET sing 374 n n 
C17 H171 RET sing 375 n n 
C17 H172 RET sing 376 n n 
C17 H173 RET sing 377 n n 
C18 H181 RET sing 378 n n 
C18 H182 RET sing 379 n n 
C18 H183 RET sing 380 n n 
C19 H191 RET sing 381 n n 
C19 H192 RET sing 382 n n 
C19 H193 RET sing 383 n n 
C20 H201 RET sing 384 n n 
C20 H202 RET sing 385 n n 
C20 H203 RET sing 386 n n 
#
_atom_sites.entry_id                     9R23 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
F 2 LFA A 1 301 301 LFA LFA . 
G 2 LFA A 1 302 302 LFA LFA . 
H 2 LFA A 1 303 304 LFA LFA . 
I 2 LFA A 1 304 307 LFA LFA . 
J 2 LFA A 1 305 309 LFA LFA . 
K 2 LFA A 1 306 312 LFA LFA . 
L 2 LFA A 1 307 313 LFA LFA . 
M 2 LFA A 1 308 314 LFA LFA . 
N 2 LFA A 1 309 315 LFA LFA . 
O 3 RET A 1 310 213 RET LYR . 
P 2 LFA A 1 311 302 LFA LFA . 
Q 2 LFA A 1 312 306 LFA LFA . 
R 2 LFA A 1 313 308 LFA LFA . 
S 2 LFA A 1 314 303 LFA LFA . 
T 2 LFA A 1 315 310 LFA LFA . 
U 2 LFA B 1 301 305 LFA LFA . 
V 2 LFA B 1 302 303 LFA LFA . 
W 2 LFA B 1 303 305 LFA LFA . 
X 2 LFA B 1 304 307 LFA LFA . 
Y 2 LFA B 1 305 312 LFA LFA . 
Z 2 LFA B 1 306 313 LFA LFA . 
AA 2 LFA B 1 307 314 LFA LFA . 
BA 2 LFA B 1 308 317 LFA LFA . 
CA 2 LFA B 1 309 318 LFA LFA . 
DA 2 LFA B 1 310 319 LFA LFA . 
EA 2 LFA B 1 311 320 LFA LFA . 
FA 2 LFA B 1 312 321 LFA LFA . 
GA 3 RET B 1 313 213 RET LYR . 
HA 2 LFA B 1 314 301 LFA LFA . 
IA 2 LFA B 1 315 303 LFA LFA . 
JA 2 LFA C 1 301 301 LFA LFA . 
KA 2 LFA C 1 302 304 LFA LFA . 
LA 2 LFA C 1 303 309 LFA LFA . 
MA 2 LFA C 1 304 316 LFA LFA . 
NA 2 LFA C 1 305 302 LFA LFA . 
OA 2 LFA C 1 306 304 LFA LFA . 
PA 2 LFA C 1 307 305 LFA LFA . 
QA 2 LFA C 1 308 308 LFA LFA . 
RA 2 LFA C 1 309 311 LFA LFA . 
SA 2 LFA C 1 310 312 LFA LFA . 
TA 2 LFA C 1 311 313 LFA LFA . 
UA 3 RET C 1 312 213 RET LYR . 
VA 2 LFA C 1 313 302 LFA LFA . 
WA 2 LFA C 1 314 314 LFA LFA . 
XA 2 LFA D 1 301 307 LFA LFA . 
YA 2 LFA D 1 302 301 LFA LFA . 
ZA 2 LFA D 1 303 303 LFA LFA . 
AB 2 LFA D 1 304 304 LFA LFA . 
BB 2 LFA D 1 305 307 LFA LFA . 
CB 2 LFA D 1 306 308 LFA LFA . 
DB 2 LFA D 1 307 309 LFA LFA . 
EB 2 LFA D 1 308 312 LFA LFA . 
FB 2 LFA D 1 309 313 LFA LFA . 
GB 2 LFA D 1 310 315 LFA LFA . 
HB 3 RET D 1 311 213 RET LYR . 
IB 2 LFA D 1 312 304 LFA LFA . 
JB 2 LFA D 1 313 306 LFA LFA . 
KB 2 LFA E 1 301 303 LFA LFA . 
LB 2 LFA E 1 302 306 LFA LFA . 
MB 2 LFA E 1 303 306 LFA LFA . 
NB 2 LFA E 1 304 301 LFA LFA . 
OB 2 LFA E 1 305 302 LFA LFA . 
PB 2 LFA E 1 306 305 LFA LFA . 
QB 2 LFA E 1 307 307 LFA LFA . 
RB 2 LFA E 1 308 309 LFA LFA . 
SB 2 LFA E 1 309 311 LFA LFA . 
TB 2 LFA E 1 310 314 LFA LFA . 
UB 2 LFA E 1 311 315 LFA LFA . 
VB 2 LFA E 1 312 316 LFA LFA . 
WB 2 LFA E 1 313 317 LFA LFA . 
XB 3 RET E 1 314 213 RET LYR . 
YB 4 HOH A 1 401 36 HOH HOH . 
YB 4 HOH A 2 402 104 HOH HOH . 
YB 4 HOH A 3 403 91 HOH HOH . 
YB 4 HOH A 4 404 6 HOH HOH . 
YB 4 HOH A 5 405 54 HOH HOH . 
YB 4 HOH A 6 406 107 HOH HOH . 
YB 4 HOH A 7 407 72 HOH HOH . 
YB 4 HOH A 8 408 98 HOH HOH . 
YB 4 HOH A 9 409 94 HOH HOH . 
ZB 4 HOH B 1 401 39 HOH HOH . 
ZB 4 HOH B 2 402 105 HOH HOH . 
ZB 4 HOH B 3 403 89 HOH HOH . 
ZB 4 HOH B 4 404 7 HOH HOH . 
ZB 4 HOH B 5 405 108 HOH HOH . 
ZB 4 HOH B 6 406 55 HOH HOH . 
ZB 4 HOH B 7 407 68 HOH HOH . 
ZB 4 HOH B 8 408 99 HOH HOH . 
ZB 4 HOH B 9 409 95 HOH HOH . 
AC 4 HOH C 1 401 40 HOH HOH . 
AC 4 HOH C 2 402 90 HOH HOH . 
AC 4 HOH C 3 403 101 HOH HOH . 
AC 4 HOH C 4 404 9 HOH HOH . 
AC 4 HOH C 5 405 109 HOH HOH . 
AC 4 HOH C 6 406 56 HOH HOH . 
AC 4 HOH C 7 407 100 HOH HOH . 
AC 4 HOH C 8 408 69 HOH HOH . 
AC 4 HOH C 9 409 53 HOH HOH . 
BC 4 HOH D 1 401 43 HOH HOH . 
BC 4 HOH D 2 402 102 HOH HOH . 
BC 4 HOH D 3 403 73 HOH HOH . 
BC 4 HOH D 4 404 10 HOH HOH . 
BC 4 HOH D 5 405 110 HOH HOH . 
BC 4 HOH D 6 406 57 HOH HOH . 
BC 4 HOH D 7 407 66 HOH HOH . 
BC 4 HOH D 8 408 96 HOH HOH . 
BC 4 HOH D 9 409 92 HOH HOH . 
CC 4 HOH E 1 401 32 HOH HOH . 
CC 4 HOH E 2 402 103 HOH HOH . 
CC 4 HOH E 3 403 8 HOH HOH . 
CC 4 HOH E 4 404 52 HOH HOH . 
CC 4 HOH E 5 405 50 HOH HOH . 
CC 4 HOH E 6 406 106 HOH HOH . 
CC 4 HOH E 7 407 97 HOH HOH . 
CC 4 HOH E 8 408 48 HOH HOH . 
CC 4 HOH E 9 409 93 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 C C1 RET . . . XB 3 132.425 126.352 89.437 1 42.66 ? C1 RET 314 E 1 
HETATM 2 C C2 RET . . . XB 3 133.086 127.185 88.325 1 47.04 ? C2 RET 314 E 1 
HETATM 3 C C3 RET . . . XB 3 133.694 128.465 88.786 1 46.11 ? C3 RET 314 E 1 
HETATM 4 C C4 RET . . . XB 3 134.731 128.175 89.849 1 44.06 ? C4 RET 314 E 1 
HETATM 5 C C5 RET . . . XB 3 134.228 127.251 90.926 1 39.75 ? C5 RET 314 E 1 
HETATM 6 C C6 RET . . . XB 3 133.194 126.397 90.75 1 38.43 ? C6 RET 314 E 1 
HETATM 7 C C7 RET . . . XB 3 132.877 125.488 91.807 1 34.46 ? C7 RET 314 E 1 
HETATM 8 C C8 RET . . . XB 3 131.909 124.548 91.85 1 35.32 ? C8 RET 314 E 1 
HETATM 9 C C9 RET . . . XB 3 131.774 123.592 92.91 1 37.25 ? C9 RET 314 E 1 
HETATM 10 C C10 RET . . . XB 3 130.815 122.602 92.866 1 36.17 ? C10 RET 314 E 1 
HETATM 11 C C11 RET . . . XB 3 130.649 121.524 93.665 1 35.94 ? C11 RET 314 E 1 
HETATM 12 C C12 RET . . . XB 3 129.682 120.557 93.414 1 40.71 ? C12 RET 314 E 1 
HETATM 13 C C13 RET . . . XB 3 129.166 119.626 94.325 1 45.03 ? C13 RET 314 E 1 
HETATM 14 C C14 RET . . . XB 3 128.158 118.785 94.019 1 54.23 ? C14 RET 314 E 1 
HETATM 15 C C15 RET . . . XB 3 127.542 117.796 94.988 1 60.91 ? C15 RET 314 E 1 
HETATM 16 C C16 RET . . . XB 3 130.971 126.768 89.686 1 44.53 ? C16 RET 314 E 1 
HETATM 17 C C17 RET . . . XB 3 132.383 124.949 88.827 1 43.76 ? C17 RET 314 E 1 
HETATM 18 C C18 RET . . . XB 3 134.971 127.409 92.225 1 34.55 ? C18 RET 314 E 1 
HETATM 19 C C19 RET . . . XB 3 132.647 123.57 94.084 1 34.51 ? C19 RET 314 E 1 
HETATM 20 C C20 RET . . . XB 3 129.756 119.668 95.653 1 52.58 ? C20 RET 314 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           20 
#